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Questions tagged [snakemake]

Snakemake is a workflow management system with a Python-style specification language.

Snakemake is a workflow management system with a Python-style specification language.

1634 questions
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snakemake --use-conda with an already created envs

I work on an SGE cluster where some tools are available with conda : source activate unicycler-0.4.7 I can use conda on my snakemake workflow with yaml, but in this way, I will going to reinstall the environment. name: unicycler channels: -…
Midoux
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shell() function in run does not use singularity

EDIT I have now posted this question as an issue on the Snakemake bitbucket given this seems to be an unknown behavior. I am using snakemake with the --use-singularity option. When I use a classic rule of the form: singularity: mycontainer rule…
Alexis
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Snakemake: Is it possible to use directories as wildcards?

Hi I´m new in Snakemake and have a question. I want to run a tool to multiple data sets. One data set represents one tissue and for each tissue exists fastq files, which are stored in the respective tissue directory. The rough command for the tools…
Rob
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Local singularity image in snakemake workflow on AWS eks with --kubernetes option

I am trying to use Snakemake on AWS EKS, running shell commands in singularity containers. If I understood correctly, Snakemake is then run as a container itself by kubernetes, so I would run a singularity container inside a Pod. I have a ubuntu…
meo
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How to fix conda "ResolvePackageNotFound" when building a conda recipe

I downloaded a conda package from github to bring a few modifications and would like to build this local package in a conda environment and test my changes. The problem is that the building of the recipe fails because conda has a…
Anoikis
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3 answers

Handling equivalent file extensions in Snakemake

Essentially, I want to know what the recomended way of handling equivalent file extensions is in snakemake. For example, lets say I have a rule that counts the number of entries in a fasta file. The rule might look something like.... rule…
Nolan Hartwick
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scriptExit 1 with pybedtools venn_mpl - snakemake 5.2.4

I want to create VennDiagramms with pybedtools. There is a special script using matplotlib called venn_mpl. It works perfectly when I try it out in my jupyter notebook. You can do it with python or using shell commands. Unfortunately something wents…
VcFbnne
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Executing checkpoint intermediate Commands

I've currently been running into some issues with snakemake running intermediate rules required by a checkpoint. After attempting to trouble shoot this issue, I believe the problem lies within the expand command in the aggregate_input function, but…
pabster212
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ambiguousruleexception in snakemake, parms crash of two branches

I have two classes of samples to be processed by different params in my first run, then merge them together in second run. like the following example: SAMPLES = ['1', '2', '3'] CLASS1 = ['1', '2'] CLASS2 = ['3'] rule all: input: …
WU Hao
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snakemake: correct syntax for accessing dictionary values

Here's an example of what I am trying to do: mydictionary={ 'apple': 'crunchy fruit', 'banana': 'mushy and yellow' } rule all: input: expand('{key}.txt', key=mydictionary.keys()) rule test: output: temp('{f}.txt') shell: …
econ
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Conditional execution of multiplexed analysis with snakemake

I've some troubles with Snakemake, up to now I didn’t found pertinent informations in the documentation (or somewhere else). In fact, I've a big file with different samples (multiplexed analyses) and I would like to stop the execution of the…
Simon
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Specifying Python version within Snakemake using script parameter

I have some code that I am incorporating into a Snakemake pipeline. I also want to be able to run the code independently of Snakemake, so I want to write flexible code. I have a config file that can be read by Snakemake and an alternative config…
berkelem
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Snakemake cluster command with mem_mb resources in multiple cluster environments (LSF, SGE)

I am moving a Snakemake workflow that I developed in an LSF cluster environment (e.g. bsub) to a SGE cluster environment (e.g. qsub). I have previously specified my jobs' memory requirements using the resources keyword in rules, using the variable…
Joseph
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How to pass variable value as input in snakemake?

I want to download the fastq files from SRA database using SRR ID using Snakemake. I read a file to get SRR ID using python code. I want to parse the Variable one by one as input. My code is below. I want to run command fastq-dump…
Himanshu Singh
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Snakemake : "wildcards in input files cannot be determined from output files"

I use Snakemake to execute some rules, and I've a problem with one: rule filt_SJ_out: input: "pass1/{sample}SJ.out.tab" output: "pass1/SJ.db" shell:''' gawk '$6==1 || ($6==0 && $7>2)' {input} >> {output}; ''' Here, I just want to…
Vincent Darbot
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